90个苹果品种耐寒性评价和全基因组关联分析

doi:10.16420/j.issn.0513-353x.2022-0052

摘要/Abstract

摘要：

以90个苹果栽培品种为试验材料，采集冬季休眠的枝条进行相对电导率测定，评价其耐寒能力；同时利用基因组重测序技术检测到的1 247 162个SNP开展全基因组关联分析，筛选与苹果耐寒性状显著关联的候选基因。鉴定出3个耐寒能力最强的品种，其相对电导率均小于40%，分别是‘金红’（‘Jinhong’），‘埃德尔博斯多夫’（‘Edelborsdorfer’），‘赫拉森’（‘Haralson’）。基于1 247 162个高质量SNP位点与表征耐寒性的相对电导率的指标的关联分析，挖掘出5个与耐寒性显著关联的SNP位点，这些位点分布在4号、15号和16号染色体上，并鉴定到与冷胁迫紧密相关的3个候选基因TIF3B1（MD04G1241100）、COR47（MD15G1003900）和MD16G1069900。

关键词: 苹果, 耐寒能力, 全基因组关联分析

Abstract:

In this study，ninety apple cultivars were used as experimental materials to evaluate cold tolerance by a relative electrical conductivity test. Genome-wide association analysis was conducted on 1 247 162 SNPs detected in apple accessions by genome resequencing technology，and candidate genes significantly associated with cold tolerance were selected. Three cultivars with the strongest cold tolerance were identified，and their relative electrical conductivity was all less than 40%，which were‘Jinhong’，‘Ederbostdorf’and‘Haralson’. Based on the association analysis using 1 247 162 high-quality SNPs and index of relative electrical conductivity characterizing cold tolerance，five significant correlated loci related to cold tolerance were identified，which were distributed on chromosome 4，15，and 16，respectively. Three candidate genes TIF3B1（MD04G1241100），COR47（MD15G1003900），and MD16G1069900 closely related to cold stress tolerance were identified.

Key words: apple, cold resistance, genome-wide association analysis

中图分类号:

S661.1

坎智勇, 张德辉, 李中兴, 余思思, 钱谦, 樊天乐, 李雪薇, 马锋旺, 管清美. 90个苹果品种耐寒性评价和全基因组关联分析[J]. 园艺学报, 2023, 50(5): 921-932.

KAN Zhiyong, ZHANG Dehui, LI Zhongxing, YU Sisi, QIAN Qian, FAN Tianle, LI Xuewei, MA Fengwang, GUAN Qingmei. Evaluation of Cold Tolerance of 90 Apple Cultivars and Genome Wide Association Analysis[J]. Acta Horticulturae Sinica, 2023, 50(5): 921-932.

图/表 8

参考文献 56

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名称 Name	电导率/% Electrical conductivity	名称 Name	电导率/% Electrical conductivity	名称 Name	电导率/% Electrical conductivity
金红Jinhong	34.43 ± 1.59	瑞丹Judaine	48.29 ± 3.16	A35	53.82 ± 3.23
埃德尔博斯多夫Edelborsdorfer	38.98 ± 1.62	Seromine	48.39 ± 1.91	北海道9号Hokkaido 9	54.78 ± 2.54
赫拉森Haralson	39.60 ± 2.26	瑞星Judestar	48.50 ± 3.86	凯密欧Cameo	55.00 ± 3.84
C32	41.19 ± 3.33	昂林Korin	49.00 ± 1.30	荷斯坦Holstein	55.52 ± 5.54
15	43.23 ± 3.43	王林Orin	49.21 ± 3.19	N1	55.52 ± 2.08
夕阳Sundowner	43.40 ± 0.38	Challenger	49.27 ± 5.12	信浓红CinanoRed	55.85 ± 3.76
蜜脆Honeycrisp	43.41 ± 0.30	弘前富士Hirosakifuji	49.36 ± 4.56	Kiku	55.85 ± 3.98
C10	43.85 ± 3.58	早红1号Early Red One	49.42 ± 2.96	玫瑰光芒Rosy Glow	55.98 ± 2.08
Ruby Mac	43.97 ± 3.63	美味Ambrosia	49.47 ± 0.49	皮诺娃Pinova	56.18 ± 2.37
Halerstadter Jungfermapfe	44.17 ± 2.98	Northfield Beauty	49.62 ± 3.39	凉香的季节Ryoka No Kisetsu	56.29 ± 3.42
Redcord	44.35 ± 1.60	Juliana	49.72 ± 3.99	皇家嘎拉Royal Gala	56.35 ± 4.72
福拉瑞娜Florina	44.37 ± 0.63	阿莱特Arlet	49.91 ± 1.45	AC	56.36 ± 1.52
魔笛Modi	44.57 ± 2.02	N7	49.95 ± 3.25	JA	56.62 ± 1.34
红勋1号Hongxun 1	44.58 ± 3.21	秋光Qiuguang	50.09 ± 0.78	千秋Senshu	56.95 ± 1.21
Yellow Transparent	44.69 ± 4.72	寒富Hanfu	50.41 ± 3.95	富士2001 Fuji 2001	57.04 ± 2.81
Chenago Strawberry	44.70 ± 2.34	Reinders	50.80 ± 3.23	鲁宾斯Rubens	57.19 ± 1.50
甘红Ganhong	45.15 ± 1.96	小国光Ralls	51.03 ± 2.92	坎兹Kanzi	57.26 ± 3.55
署红James Grieve	45.58 ± 1.62	茜Akane	51.09 ± 4.86	Gloster69	57.31 ± 1.34
晨雾Morning Mist	45.70 ± 1.69	秦阳Qinyang	51.21 ± 2.62	T22	57.33 ± 3.22
丽嘎啦 Regal Gala	46.45 ± 3.55	Goldgeld55544	51.26 ± 4.14	Chanterler	57.64 ± 1.10
1	46.50 ± 0.77	Maririi Red	51.27 ± 3.91	Su	58.38 ± 2.78
瑞林Jude-line	46.78 ± 5.88	NJ-90	51.92 ± 3.79	红盖露 Gale Gala	59.12 ± 3.90
信浓甜Cinano Sweet	47.30 ± 1.70	K296	52.62 ± 3.88	平成Heisei	59.43 ± 4.01
千秋Senshu	47.39 ± 1.60	Roho3615	53.04 ± 0.96	斯派克Spike	60.03 ± 4.67
Pound Sweet	47.98 ± 2.09	Fujiko	53.15 ± 2.80	粉金Pinkgold	60.26 ± 0.91
威廉姆斯女士Lady Williams	48.08 ± 1.90	秦冠Qinguan	53.21 ± 1.95	太平洋玫瑰Pacific Rose	60.81 ± 2.03
花嫁Wealthy	48.17 ± 3.44	凉香Ryoka	53.29 ± 4.36	红露Hongro	61.00 ± 2.96
N9	48.19 ± 4.83	阿丽亚娜Ariane	53.53 ± 1.21	大都Daitron	63.03 ± 0.32
长富2号 Nagafu 2	48.22 ± 0.80	Idared	53.68 ± 3.42	布瑞本Braeburn	64.61 ± 5.66
N2	48.25 ± 1.86	C25	53.81 ± 2.59	津轻Tsugaru	65.16 ± 5.71

名称 Name	电导率/% Electrical conductivity	名称 Name	电导率/% Electrical conductivity	名称 Name	电导率/% Electrical conductivity
金红Jinhong	34.43 ± 1.59	瑞丹Judaine	48.29 ± 3.16	A35	53.82 ± 3.23
埃德尔博斯多夫Edelborsdorfer	38.98 ± 1.62	Seromine	48.39 ± 1.91	北海道9号Hokkaido 9	54.78 ± 2.54
赫拉森Haralson	39.60 ± 2.26	瑞星Judestar	48.50 ± 3.86	凯密欧Cameo	55.00 ± 3.84
C32	41.19 ± 3.33	昂林Korin	49.00 ± 1.30	荷斯坦Holstein	55.52 ± 5.54
15	43.23 ± 3.43	王林Orin	49.21 ± 3.19	N1	55.52 ± 2.08
夕阳Sundowner	43.40 ± 0.38	Challenger	49.27 ± 5.12	信浓红CinanoRed	55.85 ± 3.76
蜜脆Honeycrisp	43.41 ± 0.30	弘前富士Hirosakifuji	49.36 ± 4.56	Kiku	55.85 ± 3.98
C10	43.85 ± 3.58	早红1号Early Red One	49.42 ± 2.96	玫瑰光芒Rosy Glow	55.98 ± 2.08
Ruby Mac	43.97 ± 3.63	美味Ambrosia	49.47 ± 0.49	皮诺娃Pinova	56.18 ± 2.37
Halerstadter Jungfermapfe	44.17 ± 2.98	Northfield Beauty	49.62 ± 3.39	凉香的季节Ryoka No Kisetsu	56.29 ± 3.42
Redcord	44.35 ± 1.60	Juliana	49.72 ± 3.99	皇家嘎拉Royal Gala	56.35 ± 4.72
福拉瑞娜Florina	44.37 ± 0.63	阿莱特Arlet	49.91 ± 1.45	AC	56.36 ± 1.52
魔笛Modi	44.57 ± 2.02	N7	49.95 ± 3.25	JA	56.62 ± 1.34
红勋1号Hongxun 1	44.58 ± 3.21	秋光Qiuguang	50.09 ± 0.78	千秋Senshu	56.95 ± 1.21
Yellow Transparent	44.69 ± 4.72	寒富Hanfu	50.41 ± 3.95	富士2001 Fuji 2001	57.04 ± 2.81
Chenago Strawberry	44.70 ± 2.34	Reinders	50.80 ± 3.23	鲁宾斯Rubens	57.19 ± 1.50
甘红Ganhong	45.15 ± 1.96	小国光Ralls	51.03 ± 2.92	坎兹Kanzi	57.26 ± 3.55
署红James Grieve	45.58 ± 1.62	茜Akane	51.09 ± 4.86	Gloster69	57.31 ± 1.34
晨雾Morning Mist	45.70 ± 1.69	秦阳Qinyang	51.21 ± 2.62	T22	57.33 ± 3.22
丽嘎啦 Regal Gala	46.45 ± 3.55	Goldgeld55544	51.26 ± 4.14	Chanterler	57.64 ± 1.10
1	46.50 ± 0.77	Maririi Red	51.27 ± 3.91	Su	58.38 ± 2.78
瑞林Jude-line	46.78 ± 5.88	NJ-90	51.92 ± 3.79	红盖露 Gale Gala	59.12 ± 3.90
信浓甜Cinano Sweet	47.30 ± 1.70	K296	52.62 ± 3.88	平成Heisei	59.43 ± 4.01
千秋Senshu	47.39 ± 1.60	Roho3615	53.04 ± 0.96	斯派克Spike	60.03 ± 4.67
Pound Sweet	47.98 ± 2.09	Fujiko	53.15 ± 2.80	粉金Pinkgold	60.26 ± 0.91
威廉姆斯女士Lady Williams	48.08 ± 1.90	秦冠Qinguan	53.21 ± 1.95	太平洋玫瑰Pacific Rose	60.81 ± 2.03
花嫁Wealthy	48.17 ± 3.44	凉香Ryoka	53.29 ± 4.36	红露Hongro	61.00 ± 2.96
N9	48.19 ± 4.83	阿丽亚娜Ariane	53.53 ± 1.21	大都Daitron	63.03 ± 0.32
长富2号 Nagafu 2	48.22 ± 0.80	Idared	53.68 ± 3.42	布瑞本Braeburn	64.61 ± 5.66
N2	48.25 ± 1.86	C25	53.81 ± 2.59	津轻Tsugaru	65.16 ± 5.71

引物名称 Primer name	正向引物（5′-3′） Forward primer	反向引物（5′-3′） Reverse primer
MD04G1241100	CAAAGAGAGGACTCATGGATACAAG	GTCCAGAAAGTGCGTTTGTAGAAC
MD15G1003900	AAGACTGAGGAGGTTCCAGTTGG	CTTCTCTTTCTCCTTGATGTCCTTG
MD16G1069900	GCTACATAGCATGAGGGACATGTTG	TCAAGCTCTGCCATGTTATCCAC

引物名称 Primer name	正向引物（5′-3′） Forward primer	反向引物（5′-3′） Reverse primer
MD04G1241100	CAAAGAGAGGACTCATGGATACAAG	GTCCAGAAAGTGCGTTTGTAGAAC
MD15G1003900	AAGACTGAGGAGGTTCCAGTTGG	CTTCTCTTTCTCCTTGATGTCCTTG
MD16G1069900	GCTACATAGCATGAGGGACATGTTG	TCAAGCTCTGCCATGTTATCCAC

染色体 Chromosome	SNP位置/bp SNP position	基因型 Genotype	SNP注释 SNP annotation	P值 P value
Chr04	31 829 140	G/A	外显子区域Exonic	3.26E-06
	31 821 706	G/A	内含子Intronic	7.21E-06
Chr15	238 509	T/C	外显子区域Exonic	5.47E-06
	7 277 652	T/C	外显子区域Exonic	8.57E-06
Chr16	4 918 081	A/G	基因间Intergenic	4.22E-06